Protein Identification and Validation

Owned by Viswanadham Sridhara

Last updated: Jul 06, 2015

1 min read

Protein Identification and Validation

Identify peptides/proteins given raw mass-spec data, 6 hour minimum ($282 internal, $360 external) per project.

1. Protein identification using Trans-Proteome Pipeline

Identify list of proteins in the sample using multiple search algorithms in Trans-Proteome Pipeline (TPP)

Deliverables:
- List of all peptide-spectral matches (no Post Translational Modifications identification). For PTM Identification, see Post-translational modification (PTM) identification

Tools Used:
- Trans-Proteome Pipeline: (http://www.proteomecenter.org/software.php)
  - XML output of all peptide and protein hits.

2. Peptide hits validation

Validate the peptide hits returned by the mass-spectrometry peptide identification algorithms

Deliverables:
- reports generated by peptideProphet

Tools Used:
- peptideProphet: (http://peptideprophet.sourceforge.net) used to validate peptide hits
  - pepXML output file that has list of validated peptide hits.

3. Protein hits validation

Validate the protein hits using the pepXML peptideProphet output

Deliverables:
- reports generated by proteinProphet

Tools Used:
- ProteinProphet: (http://proteinprophet.sourceforge.net) used to identify high-confident protein hits
  - protXML output file that has list of validated protein hits.

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